Question: How to run velvet multithreaded?
1
gravatar for SmallChess
5.1 years ago by
SmallChess510
Australia
SmallChess510 wrote:

According to http://www.ebi.ac.uk/~zerbino/velvet/, velvet can be multithreaded. But how to do it? When I do

 

./velveth

Usage:

./velveth directory hash_length {[-file_format][-read_type][-separate|-interleaved] filename1 [filename2 ...]} {...} [options]

 

My question is how to run velveth multithreaded? Where is the multi-thread flag (usually -t or -p)? I'm running 1.2.10.

metagenomics velveth • 4.0k views
ADD COMMENTlink modified 5.1 years ago by thackl2.8k • written 5.1 years ago by SmallChess510
4
gravatar for thackl
5.1 years ago by
thackl2.8k
MIT
thackl2.8k wrote:

For threading to work, Velvet has to be installed with make 'OPENMP=1'. Then you can control threading via export OMP_NUM_THREADS=7. See Velvet Manual Section 2.3.6.

ADD COMMENTlink written 5.1 years ago by thackl2.8k

Do you know if running velvet with openmp will use more memory? The manual doesn't discuss.

ADD REPLYlink written 2.6 years ago by bhanratt40

No, sorry I don't. But I think that it is not unlikely.

ADD REPLYlink written 2.6 years ago by thackl2.8k
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